How to get the median of read distribution in a genomic region?

jajclement · 05-17-2016, 07:15 AM

Hi,

I have reads aligned on my genome and a file of genomic regions (peaks from peakcalling).
I have reads falling into each regions according to a certain distribution and I would like to get the median of this distribution for each region, that is the genomic position corresponding to the median.

Do you know if an existing tool can do this ? Or do you have an idea how to compute this?

Thanks

westerman · 05-17-2016, 09:52 AM

There might be a specific tool. Aside from that, assuming you have your alignment in a BAM file then I see two methods.

1. Use the BedTools package and in particular coverageBed.

2. Use 'samtools depth' to get read depth along the reference. Put this into Excel or other spreadsheet program in order to do the median calculation.

cmbetts · 05-17-2016, 01:53 PM

The GenomicRanges package in R/Bioconductor would be well suited to this as well.

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05-17-2016, 07:15 AM	#1
jajclement Junior Member Location: Montpellier, France Join Date: May 2012 Posts: 6	How to get the median of read distribution in a genomic region? Hi, I have reads aligned on my genome and a file of genomic regions (peaks from peakcalling). I have reads falling into each regions according to a certain distribution and I would like to get the median of this distribution for each region, that is the genomic position corresponding to the median. Do you know if an existing tool can do this ? Or do you have an idea how to compute this? Thanks

05-17-2016, 09:52 AM	#2
westerman Rick Westerman Location: Purdue University, Indiana, USA Join Date: Jun 2008 Posts: 1,104	There might be a specific tool. Aside from that, assuming you have your alignment in a BAM file then I see two methods. 1. Use the BedTools package and in particular coverageBed. 2. Use 'samtools depth' to get read depth along the reference. Put this into Excel or other spreadsheet program in order to do the median calculation.

05-17-2016, 01:53 PM	#3
cmbetts Senior Member Location: Bay Area Join Date: Jun 2012 Posts: 120	The GenomicRanges package in R/Bioconductor would be well suited to this as well.